NEW TOOLS MAKE COMPLEX DATA VISIBLE TO THE NAKED EYE

AUGUST 2012

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(Posted Wed. Aug 1st, 2012)

Aug. 1: This week, Off the Cob caught up with Maize Genomics Database Curator Jack Gardiner to find out how the project has progressed over the past three months. The MGD, which is supported by the USDA ARS, is a tool being developed, with assistance from the National Corn Growers Association that will help scientists efficiently apply the knowledge gained from the Maize Genome Sequencing project to develop varieties that perform for farmers in the field.

Gardiner began by explaining that the largest development since the last update in April was the implementation of MapMan, a freely available software developed by a group at the Max Planck Institute in Germany.

“This software has improved the functionality of the database by taking the data and translating it so that we can see what genes are turned on and off,” Gardiner explained. “Then, it maps this data, translating it to show which biochemical processes are active and which ones are not. It allows us to compare and contrast data for two samples in a way that makes it easy to see differences between the two.”

Simplifying this idea, he went on to explain that MapMan takes a very large amount of data and reduces it to a smaller, more manageable amount of data. In doing so, it makes it easier to see the really important conclusions.”

“MapMan takes what we call a data reduction approach to analyzing the data,” Gardiner said. “Essentially what is does is take tens or millions of data points and reduce them down to something you can look at. It maps the data for the two samples onto known biochemical pathways. Then, it uses color projected onto a drawing of the biochemical pathway to highlight the similarities and differences between the two samples. It turns out that our eyes are very good at picking out color differences, much better than say, evaluating differences between two numbers. Essentially, MapMan uses a heat map approach to display what is going on inside the cell.”

Explaining what this type of tool could be used to develop, Gardiner noted that it might play an important role in developing drought resistance. He then explained that, while it is possible, the work to reach that point will be challenging.

“Drought is a particularly difficult problem as it is usually accompanied by high temperatures with timing and duration also playing a critical role in the final impact,” he explained. “Thus, drought is what we call a complex quantitative trait, meaning that it is controlled by a handful of genes not just a single gene. Understanding and creating truly drought resistant corn varieties will likely require a multi-pronged approach utilizing genetic engineering, physiological and genomic approaches.”

Finally, he spoke to the importance of tools like MapMan in dealing with these sorts of complex problems.

“In the area of genomic approaches, MapMan is one tool in our toolbox, which will allow us to identify which genes are key to establishing drought resistance,” Gardiner explicated. “If you take plants grown in drought and non-drought conditions, you can use MapMan to identify which genes and biochemical processes are particularly important during drought. MapMan is unique in that it ties a gene that is behaving differently during drought, to a biochemical pathway. Once we have identified crucial biochemical pathways important during drought, this allows us to look at genetic engineering or breeding approaches to create drought resistant corn. It seems likely that both of these approaches will be needed to create truly drought resistant corn.”